OxoScan - Figure 2
Quantitative profiling of plasma glycopeptides with OxoScan
## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 3.6.1 (2019-07-05)
## os macOS 10.16
## system x86_64, darwin15.6.0
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz Europe/London
## date 2022-05-30
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## package * version date lib source
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## cli 2.4.0 2021-04-05 [1] CRAN (R 3.6.2)
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##
## [1] /Library/Frameworks/R.framework/Versions/3.6/Resources/libraryRead in deglycosylation experiment data (direct from DIA-NN --extract function)
## Read in treated/untreated plasma digests
deglyco.raw <- rbind(dir_ls(raw.data.dir, regexp = "untreated") %>% ## No glycosidase treatment
fread() %>%
mutate(Exp = "- Glycosidase"), ## Add experiment condition
dir_ls(raw.data.dir, regexp = "16h") %>% ## + Glycosidase treatment
fread() %>%
mutate(Exp = "+ Glycosidase")) ## Add experiment condition
## Format longer, remove zero values, scale and add labels by each ion
deglyco <- deglyco.raw %>%
mutate(mz = ((Window.Low+Window.High)/2)) %>% ## Use middle of each m/z bin for precursor m/z plotting
select(c('RT', 'mz', 'Exp', '204.087', '366.14', '274.092')) %>%
pivot_longer(cols = 4:6,
names_to = "Ion",
values_to = "Intensity") %>% ## Make 'long' table
filter(Intensity != "0") %>% ## Remove 0 values
group_by(Ion) %>% ## Scale intensity across control/deglycosidase experiments by each ion
mutate(Scaled.Intensity = Intensity/max(Intensity)) %>%
ungroup() %>%
mutate(Ion.Label = ifelse(Ion == 274.092, ## Add labels describing oxonium ion (i.e. sugar monomer they derive from)
yes = "NeuAc",
no = ifelse(Ion == 204.087,
yes = "HexNAc",
no = "Hex+HexNAc")),
Exp = factor(Exp, levels = c("- Glycosidase", "+ Glycosidase"))) ## As factor for plottingOxonium ion map of plasma tryptic digest - Figure 2b
## Just show oxonium ion map for 204
deglyco %>%
filter(Ion == 204.087,
Exp == "- Glycosidase") %>%
ggplot(aes(x = RT,
y = mz)) +
geom_point(aes(alpha = 4*Scaled.Intensity),
size = 0.4,
shape = 15) +
theme_linedraw() +
theme(strip.background = element_blank(),
strip.text = element_text(colour = "black", face = "bold", size = 14),
panel.grid = element_blank(),
strip.text.x = element_text(hjust = -0.01),
axis.title = element_text(size = 13),
plot.margin = unit(c(1, 1, 1, 1), "cm"),
) +
scale_alpha_identity() +
scale_y_continuous(expand = expand_scale(mult = c(0, 0)),
limits = c(999,1501),
breaks = seq(1000,1500,by=100)) +
scale_x_continuous(expand = expand_scale(mult = c(0, 0)),
limits = c(5,45)) +
ylab("Precursor m/z") +
xlab("Retention Time") 
Oxonium map for all 3 ions - Figure S1b
## Format longer, remove zero values, scale and add labels by each ion
deglyco.all <- deglyco.raw %>%
filter(Exp == "- Glycosidase") %>%
mutate(mz = ((Window.Low+Window.High)/2),
.keep = "unused",
.before = 1) %>% ## Use middle of each m/z bin for precursor m/z plotting
pivot_longer(cols = 3:11,
names_to = "Ion",
values_to = "Intensity") %>% ## Make 'long' table
filter(Intensity != "0") %>% ## Remove 0 values
group_by(Ion) %>% ## Scale intensity across control/deglycosidase experiments by each ion
mutate(Scaled.Intensity = Intensity/max(Intensity)) %>%
ungroup()
## Plot faceted for each ion
deglyco.all %>%
ggplot(aes(x = RT,
y = mz)) +
geom_point(aes(alpha = 4*Scaled.Intensity),
size = 0.4,
shape = 15) +
theme_linedraw() +
theme(strip.background = element_blank(),
strip.text = element_text(colour = "black", face = "bold", size = 12, hjust = -0.01),
axis.title = element_text(size = 13),
panel.grid = element_blank(),
plot.margin = unit(c(1, 1, 1, 1), "cm"),
) +
scale_alpha_identity() +
scale_y_continuous(expand = expand_scale(mult = c(0, 0)),
limits = c(999,1501),
breaks = seq(1000,1500,by=100)) +
scale_x_continuous(expand = expand_scale(mult = c(0, 0)),
limits = c(5,45)) +
ylab("Precursor m/z") +
xlab("Retention Time") +
facet_wrap(~paste("m/z", Ion), ncol = 3)